New SP update_dc_append_comments + refresh schema and history files

HISTORY.rst

@@ -12,6 +12,7 @@ Table/column changes:
 Stored procedures:
 
 * New procedure ``update_container_dispose`` to mark a container as disposed
+* New procedure ``update_dc_append_comments`` to append text to the comments column in a data collection 
 
 Grants & roles:
 

grants/ispyb_acquisition.sql

@@ -34,6 +34,8 @@ GRANT EXECUTE ON PROCEDURE update_dc_machine TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE upsert_sample_image_analysis TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE upsert_dcg_grid TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE upsert_dc_grid TO 'ispyb_acquisition';
+
+GRANT EXECUTE ON PROCEDURE update_dc_append_comments TO 'ispyb_acquisition';
 GRANT EXECUTE ON PROCEDURE update_dc_position TO 'ispyb_acquisition';
 
 GRANT EXECUTE ON PROCEDURE `update_dc_experiment_v2` TO 'ispyb_acquisition';

schemas/ispyb/lookups.sql

@@ -207,7 +207,8 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec
 (232,'2022_09_28_ContainerType_update.sql','DONE','2022-09-28 10:04:59'),
 (233,'2022_10_17_BLSession_drop_constraint.sql','DONE','2022-10-17 11:25:35'),
 (234,'2022_10_21_Shipping_extra.sql','DONE','2022-11-02 17:04:27'),
-(235,'2022_11_02_AdminVar_bump_version.sql','DONE','2022-11-02 17:04:27');
+(235,'2022_11_02_AdminVar_bump_version.sql','DONE','2022-11-02 17:04:27'),
+(236,'2023_01_16_Tomogram_new_cols.sql','DONE','2023-01-16 18:09:03');
 /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */;
 
 /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */;

schemas/ispyb/routines.sql

@@ -7794,6 +7794,39 @@ DELIMITER ;
 /*!50003 SET character_set_results = @saved_cs_results */ ;
 /*!50003 SET collation_connection = @saved_col_connection */ ;
 /*!50003 SET @saved_sql_mode = @@sql_mode */ ;
+/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ;
+/*!50003 DROP PROCEDURE IF EXISTS `update_dc_append_comments` */;
+/*!50003 SET @saved_cs_client = @@character_set_client */ ;
+/*!50003 SET @saved_cs_results = @@character_set_results */ ;
+/*!50003 SET @saved_col_connection = @@collation_connection */ ;
+/*!50003 SET character_set_client = utf8mb3 */ ;
+/*!50003 SET character_set_results = utf8mb3 */ ;
+/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+DELIMITER ;;
+CREATE PROCEDURE `update_dc_append_comments`(
+ p_id int(11) unsigned,
+ p_comments varchar(1024),
+ p_separator varchar(5)
+)
+ MODIFIES SQL DATA
+ COMMENT 'Appends text to DataCollection.comments for dataCollectionId=p_id. '
+BEGIN
+ IF NOT (p_id IS NULL) AND NOT (p_comments IS NULL) THEN
+
+ UPDATE DataCollection 
+ SET comments = concat_ws(p_separator, comments, p_comments) 
+ WHERE dataCollectionId = p_id; 
+
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory arguments p_id and/or p_comments are NULL';
+ END IF;
+END ;;
+DELIMITER ;
+/*!50003 SET sql_mode = @saved_sql_mode */ ;
+/*!50003 SET character_set_client = @saved_cs_client */ ;
+/*!50003 SET character_set_results = @saved_cs_results */ ;
+/*!50003 SET collation_connection = @saved_col_connection */ ;
+/*!50003 SET @saved_sql_mode = @@sql_mode */ ;
 /*!50003 SET sql_mode = 'STRICT_TRANS_TABLES' */ ;
 /*!50003 DROP PROCEDURE IF EXISTS `update_dc_experiment` */;
 /*!50003 SET @saved_cs_client = @@character_set_client */ ;

schemas/ispyb/stored_programs/sp_update_dc_append_comments.sql

@@ -0,0 +1,20 @@
+DELIMITER ;;
+CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `update_dc_append_comments`(
+ p_id int(11) unsigned,
+ p_comments varchar(1024),
+ p_separator varchar(5)
+)
+MODIFIES SQL DATA
+COMMENT 'Appends text to DataCollection.comments for dataCollectionId=p_id. '
+BEGIN
+ IF NOT (p_id IS NULL) AND NOT (p_comments IS NULL) THEN
+
+ UPDATE DataCollection 
+ SET comments = concat_ws(p_separator, comments, p_comments) 
+ WHERE dataCollectionId = p_id; 
+
+ ELSE
+ SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory arguments p_id and/or p_comments are NULL';
+ END IF;
+END;;
+DELIMITER ;

schemas/ispyb/tables.sql

@@ -4043,11 +4043,21 @@ CREATE TABLE `Tomogram` (
  `xAxisCorrection` float DEFAULT NULL COMMENT 'X axis angle (etomo), unit: degrees',
  `tiltAngleOffset` float DEFAULT NULL COMMENT 'tilt Axis offset (etomo), unit: degrees',
  `zShift` float DEFAULT NULL COMMENT 'shift to center volumen in Z (etomo)',
+ `fileDirectory` varchar(255) DEFAULT NULL COMMENT 'Directory path for files referenced by this table',
+ `centralSliceImage` varchar(255) DEFAULT NULL COMMENT 'Tomogram central slice file',
+ `tomogramMovie` varchar(255) DEFAULT NULL COMMENT 'Movie traversing the tomogram across an axis',
+ `xyShiftPlot` varchar(255) DEFAULT NULL COMMENT 'XY shift plot file',
+ `projXY` varchar(255) DEFAULT NULL COMMENT 'XY projection file',
+ `projXZ` varchar(255) DEFAULT NULL COMMENT 'XZ projection file',
+ `processingJobId` int(11) unsigned DEFAULT NULL,
+ `recordTimeStamp` datetime DEFAULT current_timestamp() COMMENT 'Creation or last update date/time',
  PRIMARY KEY (`tomogramId`),
  KEY `Tomogram_fk_dataCollectionId` (`dataCollectionId`),
  KEY `Tomogram_fk_autoProcProgramId` (`autoProcProgramId`),
+ KEY `Tomogram_fk_processingJobId` (`processingJobId`),
  CONSTRAINT `Tomogram_fk_autoProcProgramId` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE SET NULL ON UPDATE CASCADE,
- CONSTRAINT `Tomogram_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE
+ CONSTRAINT `Tomogram_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT `Tomogram_fk_processingJobId` FOREIGN KEY (`processingJobId`) REFERENCES `ProcessingJob` (`processingJobId`)
 ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='For storing per-sample, per-position data analysis results (reconstruction)';
 /*!40101 SET character_set_client = @saved_cs_client */;
 DROP TABLE IF EXISTS `UserGroup`;